Several alkanethiol self-assembled monolayers (SAM), such as ethanethiol (ET), decanethiol (DT), and hexadecanethiol (HDT), were damaged by a metastable helium beam and transferred a mask pattern to the underlying gold layer with a nanoscale edge on muscovite mica. It was first found that the positive-negative inversion of the gold patterns with the DT SAM resist occur-red when the dose rate of the metastable atom increased. This inversion was caused by the contamination of the Si-containing species in the molecular pump system deposited on a gold surface when the DT SAM was completely removed. As with the DT SAM resist, negative gold patterns were fabricated with the ET SAM resist. In the case of the HDT SAM resist, we thought that the negative gold pattern resulted from the cross-linking of the main molecular chain that occurred with the polymer resist in conventional lithography. In addition, there was no relationship between the roughness and the width of the edge even when a smaller grain size was used to predict the preferred roughness. (C) 2004 Published by Elsevier B.V.